CP2K Open Source Molecular Dynamics

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exercises:2017_ethz_mmm:lennard_jones_cluster

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exercises:2017_ethz_mmm:lennard_jones_cluster [2017/02/24 16:37] – dpasseroneexercises:2017_ethz_mmm:lennard_jones_cluster [2017/02/24 16:49] – dpasserone
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 python stein.py file.xyz </code>. You will be asked the cutoff radius for the neighbors, it is **1.391** in sigma units. **You should input it in Angstrom**.  python stein.py file.xyz </code>. You will be asked the cutoff radius for the neighbors, it is **1.391** in sigma units. **You should input it in Angstrom**. 
   - before running the simulation, copy the input coordinate file into in.xyz <code>cp fcc_rand.xyz in.xyz</code>   - before running the simulation, copy the input coordinate file into in.xyz <code>cp fcc_rand.xyz in.xyz</code>
-  - run cp2k <code>module load cp2k</code>(this has only to be done once)<code>cp2k.opt -i geo_opt.inp -o geo_opt.out </code> +  - run cp2k <code>module load cp2k</code>(this has only to be done once)<code>cp2k.popt -i geo_opt.inp -o geo_opt.out </code> 
   - in the output file, note the final energy, **transform it in the unit of the paper (epsilon units)**   - in the output file, note the final energy, **transform it in the unit of the paper (epsilon units)**
   - load vmd module and play with the optimization trajectory <code>vmd OPT-pos-1.xyz</code> (ask the teacher)   - load vmd module and play with the optimization trajectory <code>vmd OPT-pos-1.xyz</code> (ask the teacher)
exercises/2017_ethz_mmm/lennard_jones_cluster.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1